US11479529B2 - Compounds with antimicrobial activity - Google Patents

Compounds with antimicrobial activity Download PDF

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US11479529B2
US11479529B2 US16/959,142 US201916959142A US11479529B2 US 11479529 B2 US11479529 B2 US 11479529B2 US 201916959142 A US201916959142 A US 201916959142A US 11479529 B2 US11479529 B2 US 11479529B2
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nusb
nuse
group
fluoro
chloro
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US20200347010A1 (en
US20210317076A9 (en
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Cong Ma
Xiao Yang
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Chinese University of Hong Kong CUHK
Hong Kong Polytechnic University HKPU
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Chinese University of Hong Kong CUHK
Hong Kong Polytechnic University HKPU
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Assigned to THE CHINESE UNIVERSITY OF HONG KONG reassignment THE CHINESE UNIVERSITY OF HONG KONG ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: YANG, XIAO
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    • C07—ORGANIC CHEMISTRY
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    • C07D231/00—Heterocyclic compounds containing 1,2-diazole or hydrogenated 1,2-diazole rings
    • C07D231/02—Heterocyclic compounds containing 1,2-diazole or hydrogenated 1,2-diazole rings not condensed with other rings
    • C07D231/10—Heterocyclic compounds containing 1,2-diazole or hydrogenated 1,2-diazole rings not condensed with other rings having two or three double bonds between ring members or between ring members and non-ring members
    • C07D231/14—Heterocyclic compounds containing 1,2-diazole or hydrogenated 1,2-diazole rings not condensed with other rings having two or three double bonds between ring members or between ring members and non-ring members with hetero atoms or with carbon atoms having three bonds to hetero atoms with at the most one bond to halogen, e.g. ester or nitrile radicals, directly attached to ring carbon atoms
    • C07D231/44—Oxygen and nitrogen or sulfur and nitrogen atoms
    • C07D231/46—Oxygen atom in position 3 or 5 and nitrogen atom in position 4
    • C07D231/50—Acylated on said nitrogen atom
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
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    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
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    • C07C215/48—Compounds containing amino and hydroxy groups bound to the same carbon skeleton having hydroxy groups bound to carbon atoms of at least one six-membered aromatic ring and amino groups bound to acyclic carbon atoms or to carbon atoms of rings other than six-membered aromatic rings of the same carbon skeleton with amino groups linked to the six-membered aromatic ring, or to the condensed ring system containing that ring, by carbon chains not further substituted by hydroxy groups
    • C07C215/50—Compounds containing amino and hydroxy groups bound to the same carbon skeleton having hydroxy groups bound to carbon atoms of at least one six-membered aromatic ring and amino groups bound to acyclic carbon atoms or to carbon atoms of rings other than six-membered aromatic rings of the same carbon skeleton with amino groups linked to the six-membered aromatic ring, or to the condensed ring system containing that ring, by carbon chains not further substituted by hydroxy groups with amino groups and the six-membered aromatic ring, or the condensed ring system containing that ring, bound to the same carbon atom of the carbon chain
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    • C07C311/44—Sulfonamides, the carbon skeleton of the acid part being further substituted by singly-bound nitrogen atoms, not being part of nitro or nitroso groups having the sulfur atom of at least one of the sulfonamide groups bound to a carbon atom of a six-membered aromatic ring having sulfur atoms of sulfonamide groups and amino groups bound to carbon atoms of six-membered rings of the same carbon skeleton having the nitrogen atom of at least one of the sulfonamide groups bound to a carbon atom of a six-membered aromatic ring
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    • C07D207/34—Heterocyclic compounds containing five-membered rings not condensed with other rings, with one nitrogen atom as the only ring hetero atom with only hydrogen or carbon atoms directly attached to the ring nitrogen atom having two double bonds between ring members or between ring members and non-ring members with hetero atoms or with carbon atoms having three bonds to hetero atoms with at the most one bond to halogen, e.g. ester or nitrile radicals, directly attached to ring carbon atoms
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Definitions

  • This invention relates to compounds having antimicrobial activity.
  • MRSA methicillin resistant Staphylococcus aureus
  • rRNA comprises up to 80% of total RNA and transcription of rRNA has been shown to positively correlate with bacterial growth rate to meet the demand for protein synthesis. 4 Although rRNA synthesis is one of the most fundamental requirements for living cells, there is a noticeable discrepancy in this process. In eukaryotic cells, the ribosonmal genes are transcribed by different types of RNA polymerases, namely, RNA Pol I, Pol II and Pol III. 5 On the other hand, there is only one RNA polymerase in bacteria, which is associated with a number of elongation factors for forming so-called “rRNA antitermination complexes”, which ensure efficient transcription of the rRNA genes. 6
  • NusB and NusE are highly conserved essential small transcription factors involved in the formation of rRNA antitermination complexes. 7
  • the protein-protein interaction between NusB and NusE represents the first regulatory step in rRNA transcription antitermination complex assembly. 8
  • other factors such as NusA, NusG, and others
  • this invention provides compounds for disruption of NusB-NusE heterodimer formation to result in reduced rates of rRNA synthesis and bacterial cell proliferation.
  • this invention provides compounds with antimicrobial activity.
  • this invention provides a compound of formula 1 or a pharmaceutically acceptable salt, prodrug, or solvate thereof:
  • this invention provides a compound of formula 2 or a pharmaceutically acceptable salt, prodrug or solvate thereof:
  • this invention provides a compound of formula 3 or a pharmaceutically acceptable salt, prodrug, or solvate thereof:
  • this invention provides a pharmaceutical composition for the treatment of a bacterial infection or a protozoal infection in mammal, fish, or bird, which comprises a therapeutically effective amount of a compound of formula 1, 2 or 3 with a pharmaceutically acceptable carrier.
  • this invention provides a method of treating a bacterial infection or a protozoal infection in a mammal, fish, or bird that comprises administering to said mammal, fish or bird a therapeutically effective amount of a compound of formula 1, 2 or 3.
  • this invention provides a method for preparing the compound of formula 1, 2, or 3.
  • treating means reversing, alleviating, inhibiting the progress of, or preventing the disorder or condition to which such term applies, or one or more symptoms of such disorder or condition.
  • treatment refers to the act of treating, as “treating” is defined immediately above.
  • bacterial infection(s) includes the following: pneumonia, otitis media, sinusitus, bronchitis, tonsillitis, and mastoiditis related to infection by Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, Staphylococcus aureus, Enterococcus faecalis, E. faecium, E. casselflavus, S. epidermidis, S.
  • haemolvticus or Peptostreptococcus spp.
  • pharyngitis rheumatic fever, and glomerulonephritis related to infection by Streptococcus pyogenes , Groups C and G streptococci, Corynebacterium diphtheriae , or Actinobacillus haemolyticum
  • respiratory tract infections related to infection by Mycoplasma pneurnoniae, Legionella pneumophila, Streptococcus pneumoniae, Haemophilus influenzae , or Chlamydia pneumoniae
  • blood and tissue infections including endocarditis and osteomyelitis, caused by S. aureus, S. haemolyticus, E.
  • strains resistant to known antibacterials such as, but not limited to, beta-lactams, vancomycin, aminoglycosides, quinolones, chloramphenicol, tetracylines and nacrolides; uncomplicated skin and soft tissue infections and abscesses, and puerperal fever related to infection by Staphylococcus aureus , coagulase-negative staphylococci (i.e., S. epidermidis, S.
  • aureus food poisoning and toxic shock syndrome
  • Groups A, B, and C streptococci ulcers related to infection by Helicobacter pylori systemic febrile syndromes related to infection by Borrelia recurrentis ; Lyme disease related to infection by Borrelia burgdorferi ; conjunctivitis, keratitis, and dacrocvstitis related to infection by Chlamydia trachomatis, Neisseria gonorrhoeae, S. aureus, S. pneumoniae, S. pyogenes, H.
  • MAC Mycobacterium avium complex
  • Bacterial infections and protozoal infections, and disorders related to such infections, which may be treated or prevented in animals include the following: bovine respiratory disease related to infection by P.
  • cow enteric disease related to infection by E. coli or protozoa i.e., coccidia, cryptosporidia, etc.
  • swine enteric disease related to infection by E. coli, Lawsonia intracellulanis, Salmonella , or Serpulina hyodysinteniae ; cow footrot related to infection by Fusobacterium spp.; cow metritis related to infection by E coil; cow hairy warts related to infection by Fusobacterium necrophorum or Bacteroides nodosus ; cow pink-eye related to infection by Moraxella bovis ; cow premature abortion related to infection by protozoa (i.e. neosporium); urinary tract infection in dogs and cats related to infection by E.
  • protozoa i.e. neosporium
  • halo includes fluoro, chloro, bromo or iodo.
  • Preferred halo groups are fluoro, chloro and bromo.
  • alkyl includes saturated monovalent hydrocarbon radicals having cyclic, straight and/or branched moieties. It is to be understood that to include cyclic moieties, the alkyl group must include at least 3 carbon atoms.
  • alkenyl as used herein, unless otherwise indicated, includes alkyl groups as defined above having at least one carbon-carbon double bond at some point in the alkyl chain.
  • alkynyl as used herein, unless otherwise indicated, includes alkyl groups as defined above having at least one carbon-carbon triple bond at some point in the alkyl chain.
  • aryl includes an organic radical derived from an aromatic hydrocarbon by removal of one hydrogen, such as phenyl or naphthyl.
  • the term “4 to 10 membered heterocyclic” includes aromatic and non-aromatic heterocyclic groups containing one or more heteroatoms each selected from O, S and N, wherein each heterocyclic group has from 4 to 10 atoms in its ring system.
  • Non-aromatic heterocyclic groups include groups having only 4 atoms in their ring system, but aromatic heterocyclic groups must have at least 5 atoms in their ring system.
  • the heterocyclic groups include benzo-fused ring systems and ring systems substituted with one or more oxo moieties.
  • An example of a 4 membered heterocyclic group is azetidinyl (derived from azetidine).
  • An example of a 5 membered heterocyclic group is thiazolyl and an example of a 10 membered heterocyclic group is quinolinyl.
  • Examples of non-aromatic heterocyclic groups are pyrrolidinyl, tetrahydrofuranyl, tetrahydrothienyl, tetrahydropyranyl, tetrahydrothiopyranyl, piperidino, morpholino, thiomorpholino, thioxanyl, piperazinyl, azetidinyl, oxetanyl thietanyl, homopiperidinyl, oxepanyl, thiepanyl, oxazepinyl, diazepinyl, thiazepinyl, 1,2,3,6-tetrahydropyridinyl, 2-pyrrolinyl, 3-pyrrolinyl, indolinyl, 2H-pyranyl, 4H-pyranyl,
  • aromatic heterocyclic groups are pyridinyl, imidazolyl, pyrimidinyl, pyrazolyl, triazolyl, pyrazinyl, tetrazolyl, furyl, thienyl, isoxazolyl, thiazolyl, oxazolyl, isothiazolyl, pyrrolyl, quinolinyl, isoquinolinyl, indolyl, benzimidazolyl, benzofuranyl, cinnolinyl, indazolyl, indolizinyl, phthalazinyl, pyridazinyl, triazinyl, isoindolyl, pteridinyl purinyl, oxadiazolyl, thiadiazolyl, furazanyl, benzofurazanyl.
  • benzothiophenyl benzothiazolyl, benzoxazolyl, quinazolinyl, quinoxalinyl, naphthyridinyl, and furopyridinyl.
  • the foregoing groups may be C-attached or N-attached where such is possible.
  • a group derived from pyrrole may be pyrrol-1-yl (N-attached) or pyrrol-3-yl (C-attached).
  • the phrase “pharmaceutically acceptable salt(s)” includes salts of acidic or basic groups which may be present in the compounds of formula 1, 2 or 3.
  • the compounds of formula 1, 2 or 3 that are basic in nature are capable of forming a wide variety of salts with various inorganic and organic acids.
  • acids that may be used to prepare pharmaceutically acceptable acid addition salts of such basic compounds of formula 1, 2 or 3 are those that form non-toxic acid addition salts, i.e., salts containing pharmacologically acceptable anions, such as the acetate, benzenesulfonate, benzoate, bicarbonate, bisulfate, bitartrate, borate, bromide, calcium edetate, camsylate, carbonate, chloride, clavulanate, citrate, dihydrochloride, edetate, edislyate, estolate, esylate, ethylsuccinate, fumarate, gluceptate, gluconate, glutamate, glycollylarsanilate, hexylresorcinate, hydrabamine, hydrobromide, hydrochloride, iodide, isothionate, lactate, lactobionate, laurate, malate, maleate, mandelate, mesylate, methyl
  • FIG. 1A Model of the bacterial rRNA transcription complex.
  • FIG. 1B NusB-NusE interface.
  • FIG. 2A Pharmacophore model with MC4 docked in.
  • FIG. 2B Chemical structure of (E)-2- ⁇ [3-ethynylphenyl)imino]methyl ⁇ -4-nitrophenol (MC4).
  • FIG. 3 Antimicrobial activity of MC4 against selected pathogenic bacteria. Abbreviations: MIC, minimum inhibitory concentration; MBC, minimum bactericidal concentration; ND, not determined.
  • FIG. 4 Effects of MC4, rifampicin (Rif), and oxacillin (Oxa) at one-quarter minimum inhibitory concentrations (MICs) on DNA, rRA (16S+23S), and protein production in S. aureus 25923 cells.
  • FIG. 5 Partial sequence alignments of NusB and NusE.
  • Aaeo Aquifex aeolicus ;
  • Bsub Bacillus subtilis ;
  • Ecol Escherichia coli ;
  • Hinf Haemophilus influenzae ;
  • Hpyl Helicobacter pylori ;
  • Paer Pseudomonas aeruginosa ;
  • Mtub Mycobacterium tuberculosis ; Saur: Staphylococcus aureus ; Spne: Streptococcus pneumoniae ;
  • Arrow indicates residues involved in NusB-E interaction.
  • FIG. 6 Seven compounds short listed from in silico screening.
  • MC1 N- ⁇ 4-[2-(2-nitrobenzoyl)carbohydrazonoyl]phenyl ⁇ acetamide (CAS no. 679423-05-3)
  • MC2 3-( ⁇ 4-[(1,5-dimethyl-3-oxo-2-phenyl-2,3-dihydro-1H-pyrazol-4-yl)sulfamoyl]phenyl ⁇ carbamoyl)propanoic acid (CAS no. 253605-53-7);
  • MC3 3-[3-(3-hydroxy-4H-pyrazol-4-yl)propyl]-1-(4-methoxyphenyl)thiourea (CAS no.
  • MC6 N-(4- ⁇ [2-(2,4-dichlorophenoxy)phenyl]sulfamoyl ⁇ phenyl)-3,4-dimethoxybenzene-1-sulfonamide (CAS no. 312324-35-9); MC7, methyl 4-[(1E)-[(E)-2- ⁇ [4-(methoxycarbonyl)-2,5-dimethyl-1H-pyrrol-3-yl]methylidene ⁇ hydrazin-1-ylidene]methyl]-2,5-dimethyl-1H-pyrrole-3-carboxylate (CAS no. 883037-11-4).
  • FIG. 7 Ten analogues of MC4.
  • MC4-1 2-nitro-6-[(E)-(phenylimino)methyl]phenol (CAS no. 243981-87-5);
  • MC42 2- ⁇ 1[(1E)-(2-hydroxy-3-nitrophenyl)methylene]amino ⁇ -4-methylphenol (CAS no. 321726-90-3);
  • MC4-3 1-(3- ⁇ [(1E)-(2-hydroxy-5-nitrophenyl)methylene]amino ⁇ phenyl)ethanone (CAS no. 316133-49-0);
  • MC4-4 4-nitro-2-[(phenylimino)methyl]phenol (CAS no.
  • MC4-5 2- ⁇ (E)-[(3-methylphenyl)imino]methyl ⁇ -4-nitrophenol (CAS no. 303058-73-3); MC4-6, 2- ⁇ (E)-[(4-hydroxyphenyl)imino]methyl ⁇ -4-nitrophenol (CAS no. 1081780-22-4); MC4-7, 2- ⁇ (E)-[(4-chlorophenyl)imino]methyl ⁇ -4-nitrophenol (CAS no. 303215-49-8); MC4-8, 2- ⁇ (E)[(3-hydroxyphenyl)imino]methyl ⁇ -4-nitrophenol (CAS no. 303215-19-2).
  • FIG. 9 shows the minimum inhibitory concentration of MC4 analogues on various microorganisms.
  • the present invention relates to compounds of formula 1, 2 or 3 having anti-bacterial activity.
  • those compounds of the formula 1, 2 or 3 that are acidic in nature are capable of forming base salts with various pharmacologically acceptable cations.
  • Examples of such salts include the alkali metal or alkaline earth metal salts and particularly, the sodium and potassium salts.
  • certain compounds of formula 1, 2 or 3 may have asymmetric centers and therefore exist in different enantiomeric forms.
  • This invention relates to the use of all optical isomers and stereoisomers of the compounds of formula 1, 2 or 3 and mixtures thereof.
  • the invention includes both the E and Z isomers of the compound.
  • the invention includes tautomers of the compounds of formula 1, 2 or 3.
  • the present invention also includes isotopically-labelled compounds, and the pharmaceutically acceptable salts thereof, which are identical to those recited in formula 1, 2 or 3, but for the fact that one or more atoms are replaced by an atom having anatomic mass or mass number different from the atomic mass or mass number usually found in nature.
  • isotopes that can be incorporated into compounds of the invention include isotopes of hydrogen, carbon, nitrogen, oxygen, phosphorous, fluorine and chlorine, such as 2H, 3H, 13C, 14C, 15N, 180, 170, 35S, 18F, and 36C, respectively.
  • Compounds of the present invention, prodrugs thereof, and pharmaceutically acceptable salts of said compounds or of said prodrugs which contain the aforementioned isotopes and/or other isotopes of other atoms are within the scope of this invention.
  • Certain isotopically-labelled compounds of the present invention, for example those into which radioactive isotopes such as 3H and 14C are incorporated, are useful in drug and/or substrate tissue distribution assays. Tritiated, i.e, 3H, and carbon-14, i.e., 14C, isotopes are particularly preferred for their ease of preparation and detectability.
  • Isotopically labelled compounds of formula 1, 2 or 3 of this invention and prodrugs thereof can generally be prepared by carrying out the procedures disclosed in the Schemes and/or in the Examples and Preparations below, by substituting a readily available isotopically labelled reagent for a non-isotopically labelled reagent.
  • this invention also encompasses pharmaceutical compositions containing, and methods of treating bacterial infections through administering, prodrugs of compounds of the formula 1, 2 or 3.
  • Compounds of formula 1, 2 or 3 having free amino, amido, hydroxy or carboxylic groups can be converted into prodrugs.
  • Prodrugs include compounds wherein an amino acid residue, or a polypeptide chain of two or more (e.g., two, three or four) amino acid residues is covalently joined through an amide or ester bond to a free amino, hydroxy or carboxylic acid group of compounds of formula 1, 2 or 3.
  • the amino acid residues include but are not limited to the 20 naturally occurring amino acids commonly designated by three letter symbols and also includes 4-hydroxyproline, hydroxylysine, demosine, isodemosine, 3-methylhistidine, norvalin, beta-alanine, gamma-aminobutyric acid, citrulline homocysteine, homoserine, omithine and methionine sulfone. Additional types of prodrugs are also encompassed. For instance, free carboxyl groups can be derivatized as amides or alkyl esters.
  • Free hydroxy groups may be derivatized using groups including but not limited to hemisuccinates, phosphate esters, dimethylaminoacetates, and phosphoryloxymethyloxycarbonyls, as outlined in Advanced Drug Delivery Reviews, 1996, 19, 115.
  • Carbamate prodrugs of hydroxy and amino groups are also included, as are carbonate prodrugs, sulfonate esters and sulfate esters of hydroxy groups.
  • acyl group may be an alkyl ester, optionally substituted with groups including but not limited to ether, amine and carboxylic acid functionalities, or where the acyl group is an amino acid ester as described above, are also encompassed.
  • Prodrugs of this type are described in J. Med. Chem. 1996, 39, 10. Free amines can also be derivatized as amides, sulfonamides or phosphonamides. All of these prodrug moieties may incorporate groups including but not limited to ether, amine and carboxylic acid functionalities.
  • the compounds of the present invention may have asymmetric carbon atoms.
  • Diastereomeric mixtures can be separated into their individual diastereomers on the basis of their physical chemical differences by methods known to those skilled in the art, for example, by chromatography or fractional crystallization.
  • Enantiomers can be separated by converting the enantiomeric mixtures into a diastereomeric mixture by reaction with an appropriate optically active compound (e.g., alcohol), separating the diastereomers and converting (e.g., hydrolyzing) the individual diastereomers to the corresponding pure enantiomers. All such isomers, including diastereomeric mixtures and pure enantiomers, are considered as part of the invention.
  • Any compounds of formula 1, 2 or 3 that are basic in nature are capable of forming a wide variety of salts with various inorganic and organic acids.
  • any compounds of the formula 1, 2 or 3 that are acidic in nature are capable of forming base salts with various pharmacologically acceptable cations.
  • examples of such salts include the alkali metal or alkaline-earth metal salts and particularly, the sodium and potassium salts. These salts may be prepared by conventional techniques.
  • the chemical bases which are used as reagents to prepare the pharmaceutically acceptable base salts of this invention are those which form non-toxic base salts with any acidic compounds of formula 1, 2 or 3.
  • Such non-toxic base salts include those derived from such pharmacologically acceptable cations as sodium, potassium calcium and magnesium, etc.
  • salts can be prepared by treating the corresponding acidic compounds with an aqueous solution containing the desired pharmacologically acceptable cations, and then evaporating the resulting solution to dryness, preferably under reduced pressure.
  • they may also be prepared by mixing lower alkanolic solutions of the acidic compounds and the desired alkali metal alkoxide together, and then evaporating the resulting solution to dryness in the same manner as before.
  • stoichiometric quantities of reagents are preferably employed in order to ensure completeness of reaction and maximum yields of the desired final product.
  • the compounds of formula 1, 2 or 3, and the pharmaceutically acceptable salts and solvates thereof may be administered through oral, parenteral, topical, or rectal routes in the treatment or prevention of bacterial or protozoal infections. Variations may nevertheless occur depending upon the species of mammal, fish or bird being treated and its individual response to said medicament, as well as on the type of pharmaceutical formulation chosen and the time period and interval at which such administration is carried out.
  • the active compounds may be administered alone or in combination with pharmaceutically acceptable carriers or diluents by the routes previously indicated, and such administration may be carried out in single or multiple doses. More particularly, the active compounds may be administered in a wide variety of different dosage forms, i.e., they may be combined with various pharmaceutically acceptable inert carriers in the form of tablets, capsules, lozenges, troches, hard candies, powders, sprays, creams, salves, suppositories, jellies, gels, pastes, lotions, ointments, aqueous suspensions, injectable solutions, elixirs, syrups, and the like.
  • Such carriers include solid diluents or fillers, sterile aqueous media and various non-toxic organic solvents, etc.
  • oral pharmaceutical compositions can be suitably sweetened and/or flavored.
  • the active compounds are present in such dosage forms at concentration levels ranging from about 5.0% to about 70% by weight.
  • tablets containing various excipients such as microcrystalline cellulose, sodium citrate, calcium carbonate, dicalcium phosphate and glycine may be employed along with various disintegrants such as starch (and preferably corn, potato, or tapioca starch), alginic acid and certain complex silicates, together with granulation binders like polyvinylpyrrolidone, sucrose, gelatin and acacia.
  • lubricating agents such as magnesium stearate, sodium lauryl sulfate and talc are often very useful for tabletting purposes
  • Solid compositions of a similar type may also be employed as fillers in gelatin capsules; preferred materials in this connection also include lactose or milk sugar as well as high molecular weight polyethylene glycols.
  • the active compound may be combined with various sweetening or flavoring agents, coloring matter or dyes, and, if so desired, emulsifying and/or suspending agents as well, together with such diluents as water, ethanol, propylene glycol, glycerin and various like combinations thereof.
  • solutions of an active compound in either sesame or peanut oil or in aqueous propylene glycol may be employed.
  • the aqueous solutions should be suitably buffered (preferably pH greater than 8) if necessary and the liquid diluent first rendered isotonic.
  • These aqueous solutions are suitable for intravenous injection purposes.
  • the oily solutions are suitable for intraarticular, intramuscular and subcutaneous injection purposes. The preparation of all these solutions under sterile conditions is readily accomplished by standard pharmaceutical techniques will known to those skilled in the art.
  • the active compounds may be administered in the feed of the animals or orally as a drench composition.
  • the active compounds may also be administered in the form of liposome delivery systems, such as small unilamellar vesicles, large unilamellar vesicles and multilamellar vesicles.
  • liposomes can be formed from a variety of phospholipids, such as cholesterol, stearylamine or phosphatidylcholines.
  • the active compounds may also be coupled with soluble polymers as targetable drug carriers.
  • soluble polymers can include polyvinylpyrrolidone, pyran copolymer, polyhydroxypropylmethacrylamide phenyl, polyhydroxyethylaspartamide-phenol, or polyethyleneoxide-polylysine substituted with palmitoyl residues.
  • the active compounds may be coupled to a class of biodegradable polymers useful in achieving controlled release of a drug, for example, polylactic acid, polyglycolic acid, copolymers of polylactic and polyglycolic acid, polyepsilon caprolactone, polyhydroxy butyric acid, polyorthoesters, polyacetals, polydihydropyrans, polycyanoacrylates and cross-linked or amphipathic block copolymers of hydrogels.
  • a drug for example, polylactic acid, polyglycolic acid, copolymers of polylactic and polyglycolic acid, polyepsilon caprolactone, polyhydroxy butyric acid, polyorthoesters, polyacetals, polydihydropyrans, polycyanoacrylates and cross-linked or amphipathic block copolymers of hydrogels.
  • the present invention provides a compound of formula 1,
  • the present invention provides a compound including but not limited to:
  • the present invention provides a compound including but not limited to:
  • the present invention provides a pharmaceutical composition for treatment or prevention of bacterial or protozoal infections, comprising the compound.
  • the composition is in the form of tablets, capsules, lozenges, troches, hard candies, powders, sprays, creams, salves, suppositories, jellies, gels, pastes, lotions, ointments, aqueous suspensions, injectable solutions, elixirs, or syrups.
  • the pharmaceutical composition comprises 5% to 70% by weight of the compound.
  • the bacterial or protozoal infections are caused by microorganism selected from the group consisting of Enterococcus faecalis, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter cloacae, Escherichia coli , and Streptococcus pneumoniae.
  • the present invention provides a method to inhibit NusB-NusE interaction in a microorganism, comprising the step of contacting the compound with said microorganism.
  • the NusB is selected from NusB E81, NusB Y18 and NusB E75, and NusE is selected from NusE H15, NusE D19, and NusE R16.
  • the microorganism is selected from the group consisting of Enterococcus faecalis, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter cloacae, Escherichia coli , and Streptococcus pneumoniae.
  • the present invention provides a method of treating or preventing bacterial or protozoal infections in a subject, comprising a step of administering a therapeutically effective amount of the compound to said subject.
  • the compound is administered through an oral, parenteral, topical, or rectal route.
  • the microorganism is selected from the group consisting of Enterococcus faecalis, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter cloacae, Escherichia coli , and Streptococcus pneumoniae.
  • the NusB is selected from NusB E81, NusB Y18 and NusB E75, and NusE is selected from NusE 1-15, NusE D19 and NusE R16.
  • the present invention provides a compound of formula 2,
  • the compound is selected from the group consisting of:
  • the present invention provides a compound of formula 3,
  • the compound is N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl-N-(2-aminoethyl)-2-aminoethyl
  • a bacterial rRNA transcription complex was modeled on the basis of the crystal structure of the RNA polymerase elongation complex 13 with a suite of Nus transcription factors NusA, NusB, NusE, and NusG ( FIG. 1A ).
  • NusG binds to the central cleft of RNA polymerase via its N-terminal domain, 14 and its Cterminal domain interacts with NusE, 15 which anchors the NusB-NusE-boxA subcomplex to the downstream face of RNA polymerase ( FIG. 1A ).
  • NusA binds to RNA polymerase near the RNA exit channel ( FIG. 1A ), 16 consistent with its binding to rRNA just downstream of the boxA sequence.
  • FIG. 1B Examination of the published crystal structures of the Escherichia coli NusB-NusE heterodimer [Protein Data Bank (PDB) entry 3D3B] ( FIG. 1B ) 21 reveals that NusE contains only 18% ⁇ -helix and binds with NusB mainly via interactions with helix 2 ( FIG. 1B ). 22 The hydrogen bonding interactions occur between NusB E81 and NusE H15, NusB Y18 and NusE D19, and NusB E75 and NusE. R16 ( FIG. 1B , expanded view; E. coli amino acid residue numbering), which are highly conserved across prokaryotes ( FIG. 5 , arrows). Additionally, a nuclear magnetic resonance study of the Aquifex aeolicus NusB-NusE interaction also confirmed similar interactions exist in solution. 23
  • the structural information about the NusB-NusE heterodimer co-crystal (PDB entry 3D3B) 22 was used to develop a pharmacophore model ( FIG. 2A ).
  • the pharmacophore model comprised two hydrogen donors (pink), one acceptor (green) to mimic the major hydrogen bonds between NusB and NusE as mentioned above, and one conserved hydrophobic interaction (cyan, FIG. 2A ) between E. coli residues NusB L22 and NusE V26.
  • cyan cyan
  • a series of exclusion zones (gray) were added to minimize steric clashes within the shallow pocket that forms the binding site on NusB.
  • the final pharmacophore model was then created using Biovia DS4.5 to map on all the features required.
  • an in silico screen was performed using a virtual compound library constructed by combining the mini-Maybridge library and the Enamine antibacterial library. 25 The top 50 hits from the initial virtual screen were re-mapped against the pharmacophore model and the energy-minimized conformations of compounds visually inspected. The compounds that poorly fit into the pharmacophore were removed. As a result, seven compounds ( FIG. 6 ) were initially short-listed for wet-laboratory testing.
  • MC4 The antimicrobial activity of the seven compounds against community-acquired MRSA strain USA300 were first screened. Of the analogues evaluated, MC4 ( FIG. 2B ) was found to demonstrate growth inhibition effects with a minimum inhibitory concentration (MIC) of 64 ⁇ g/mL ( FIG. 3 ). With a molecular weight of 266.3, MC4 has been reported to be of use only to form a metal complex dye in optical layers for optical data recording. 26 The antimicrobial activities of MC4 against a panel of representative strains of pathogens were then tested. MC4 demonstrated preferred antimicrobial activity against S. aureus strains, including MRSA, over other pathogens tested, with MICs as low as 8 ⁇ g/mL against control strain S. aureus 25923 and 16 g/mL against healthcare acquired MRSA ST239 ( FIG. 3 ). Additionally, MC4 did not show significant cytotoxicity against mammalian cell lines compared to 5-fluorouracil (Table 1).
  • MC4 showed a significant reduction in the rRNA level, which was lower than that of rifampicin treated cells ( FIG. 4 ). Furthermore, MC4 treatment led to a significant reduction in the protein level, while rifampicin did not show this effect, probably as a result of a decreased level of ribosome production, affecting the protein synthesis ability. Oxacillin-treated cells displayed rRNA and protein production levels slightly higher than those of control cells.
  • MC4 transcription factors that are required for the formation of highly processive complexes used for the synthesis of rRNA within bacterial cells was targeted.
  • One of the short-listed compounds (MC4) showed specific activity against S. aureus strains, including MRSA, without significant toxicity to mammalian cell lines. This compound is like the first designed to target bacterial rRNA synthesis that has antimicrobial activities. The detailed effect of MC4 in rRNA transcription/processing, ribosome biogenesis, and S. aureus virulence is currently under investigation.
  • MC4 has been shown to specifically inhibit NusB-NusE interaction at the molecular level, any potential off-target effect on bacterial cells remains to be elucidated. Because NusB and NusE are highly conserved in bacteria, the reason that MC4 has preferred antimicrobial activity against S. aureus over other pathogens needs to be further investigated.
  • Bacterial Strains and Chemicals The following bacterial strains were used in this study for the microdilution assay: Enterococcus faecalis ATCC 29212, Klebsiella pneumonia ATCC 700603, Acinetobacter baumannii ATCC 19606, Pseudomonas aeruginosa PA01, Enterobacter cloacae ATCC 13047, E. coli ATCC 25922, Proteus vulgaris ATCC 6380, and S. aureus USA300, ATCC 25923, ATCC 29213, ST22, ST30, ST45, ST59, ST239, JE-2, BAA44. E.
  • coli strain DH5a (Gibco BRL) was used in this study for cloning and BL21 (DE3) pLysS 23 was used for protein overproduction.
  • 5-fluorouracil, rifampicin and other antibiotics used in the microdilution assay were purchased from SigmaAldrich.
  • Compounds MC1-7 were purchased from MolPort.
  • the antitermination complex model was constructed by consolidating a number of published crystal structures, including the Thermus thermophilus transcription elongation complex (PDB: 2O5I), 34 E. coli RNA polymerase-NusG complex (PDB: 5 tbz), 35 Aquifex aeolicus NusB-E in complex with boxA RNA (PDB: 3R2C), Mycobacterium tuberculosis NusA C-terminal domain-RNA complex (PDB: 2ASB); 37 as well as the NMR solution structure of E. coli NusE:NusG-CTD complex (PDB: 2KVQ), 38 and B. subtilis NusA N-terminal domain (PDB: 2MT4). 39 Structure matching was performed using the MatchMaker function of UCSF Chimera. 40 Images were generated with UCSF Chimera.
  • Microdilution assay was performed according to the Clinical & Laboratory Standards Institute recommendations. 42 Serial 2-fold dilutions of the tested compounds and antibiotic controls were made from 256 ⁇ g/ml to 0.5 ⁇ g/ml. DMSO was included as a negative control.
  • Cytotoxicity assay was performed as detailed previously 43 except A549 lung carcinoma and HaCaT immortalized human keratinocytes were used in this study.
  • DNA and protein quantitation 1 ml cells were harvested and treated with 10 mg/ml lysozyme+0.5 mg/ml lysostaphin at RT for 1 hr before centrifugation at 13000 g/min for 3 min.
  • RNA quantitation 1 ml culture was collected and treated with RNAProtect (Qiagen), before total RNA was extracted with an RNeasv Mini Kit (Qiagen). DNase I treatment was performed with a TURBO DNA-free Kit (ThermoFisher). The extracted RNA was subjected to Agilent 2100 analysis, and the level of major rRNA (the sum of 16S+23S rRNA) as percentage of total RNA. The values were compared across each treatment group. All experiments were repeated three times.
  • B. subtilis nusB was amplified using primers 5′-AAAGGAGATCTAGACATGAA AGAAGA-3′ (SEQ ID NO: 1) and 5′TTTTCTGGTACCCTATGATT CCC-3′AMD (SEQ ID NC: 2) from purified B. subtilis chromosomal DNA.
  • the nusB mutants were made by PCR splicing 44 using mutant primers 5′-CTT CAGGCACIAgc 5′-CTTTGCAGGCACTAgcTCA AATTGATGTC-3′ (SEQ ID NO: 3) and 5′ GACATCAATTTGAgcTAGTG CCTGCAAAG-3′ (SEQ ID NO: 4), 5′-GAATTGGAAGCTCGATgcGATTGCCAATG-3′ (SEQ ID NO: 5) and 5′-CATTGGCAATCgcATCGA GCTTCCAATTC-3′ (SEQ ID NO: 6), and 5′GATTGCCAATGTTGCCCGTG CGATTTTGC-3′ (SEQ ID NO: 7) and 5′-GCAAAATCGCACGGgCAAC ATTGGCAATC-3′ (SEQ ID NO: 8)
  • the amplicons were cut with XbaI and Acc65I and inserted into similarly cut pETMCSIII (Table 2) to produce pNG130, pNG1178, p
  • B. subtilis nusE was amplified using primers 5′-AAGGAGGGTCTAGAATGGCAAAAC-3′ (SEQ ID NO: 9) and 5′ CTATATTTTAGGTACCAAGT TTAATTT-3′ (SEQ ID NO: 10) from B. subtilis chromosomal DNA and ligated into the NdeI and Acc65I sites of pNG651 to give pNG896 (Table 2).
  • B. subtilis NusB wild type and mutant
  • NusE-GST were overproduced from plasmids (Table 2) and purified using a similar approach to that described previously. 45 Purified proteins were dialyzed into 20 mM KH2PO4, 150 mM NaCl, 30% glycerol, pH 7.8 and stored at 80° C.
  • ELISA-based assays were performed as described previously, 41 except NusB was used to coat the NUNC MaxiSorpTM 96-well plates and GST-tagged NusE used as the probe.
  • ITC Isothermal calorimetric titration
  • nusE cloned into XbaI and Acc65I cut pETMCSIII pNG896 bla P ⁇ 10 -nusE-3CGST-T ⁇ This work.
  • nusB (F15A) cloned into XbaI and Acc65I cut pETMCSIII pNG1179 blaP ⁇ 10 -6xHis-nusB (R70A) -T ⁇ This work.
  • nusB (D75A) cloned into XbaI and Acc65I cut pETMCSIII bla cat, ampicillin and chloramphenicol resistance gene
  • P ⁇ 10 phage T7 promoter
  • P xyl xylose inducible promoter, T ⁇ , T7 transcription terminator
  • 3C the recognition sequence of 3C protease
  • GST Glutathione S-transferase
  • PKA protein kinase A recognition site.
  • FIG. 9 The structures of further MC4 analogues are presented below with their minimum inhibitory concentrations on 9 microorganisms are shown in FIG. 9 (EFAE 19433: Enterococcus faecalis ATCC 19433:SAUR 25923: Staphylococcus aureus ATCC 25923; SAUR 29213; Staphylococcus aureus ATCC 29213; KPNE 700603: Klebsiella pneumoniae ATCC 700603; ABAU 19606: Acinetobacter baumannii ATCC 19606; PAER 27853: Pseudomonas aeruginosa AFCC 27853; ECLO 13047: Enterobacter cloacae ATCC 13047; ECOL 25922: Escherichia coli ATCC 25922; SPNE 49619: Streptococcus pneumoniae ATCC 49619).
  • the antimicrobial activity of the compounds was determined by broth microdilution according to the CLSI guidelines (1).
  • the test medium was cation-adjusted Mueller-Hinton broth (MH).
  • MH Mueller-Hinton broth
  • Serial two-fold dilutions were performed for the tested chemicals starting from 256 ⁇ g/ml to 0.0625 ⁇ g/ml, and the bacterial cell inoculum was adjusted to approximately 5 ⁇ 105 CFU per ml. Results were taken after 20 h of incubation at 37° C. MIC was defined as the lowest concentration of antibiotic with no visible growth. Experiments were performed in duplicates.

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